MolNFT v1 · #124937 · protein

Expanded poliovirus in complex with vhh 7A

5KU2 · VP1: “Expanded poliovirus in complex with vhh 7A”. Electron microscopy, 9 pockets (best druggability 0.77). MolNFT v1 #124937 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KU2
Type: protein
Length: 771 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3; Vhh 7A
UniProt: P03300
Pockets: 9 · best druggability 0.77

Structure

electron microscopy · 4 distinct chains · 9% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	VP1	protein	191	7% helix, 39% strand	P03300
2	VP2	protein	235	13% helix, 35% strand	P03300
3	VP3	protein	221	11% helix, 29% strand	P03300
7	Vhh 7A	protein	124	2% helix, 34% strand	—

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	440	0.77	0.86	64	empty
2	439	0.63	0.77	64	empty
3	265	0.49	0.74	34	empty
4	81	0.47	0.81	14	empty
5	61	0.46	0.83	18	empty

Interfaces

4 interfaces between chains.

1–3 · 2055 Å² buried · 29 hydrogen bonds · protein-protein
2–3 · 1583 Å² buried · 18 hydrogen bonds · protein-protein
1–2 · 1250 Å² buried · 14 hydrogen bonds · protein-protein
3–7 · 984 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5KU2 · expanded poliovirus in complex with VHH 7A · the same entry in another collection · chain 1 against 1, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P03300
Elsewhere: RCSB PDB 5KU2 · PDBe 5KU2 · UniProt P03300

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